fitted.graph-class: S4 class to represent a population tree or admixture graph...

In poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data

S4 class to represent a population tree or admixture graph and its underlying fitted parameter.

Description

S4 class to represent a population tree or admixture graph and its underlying fitted parameter.

Details

The dot.graph element allows to plot the graph using grViz() from the DiagrammeR package or with the dot program after writing the files (e.g., dot -Tpng inputgraph.dot in terminal). Note that the dot file may be customized (e.g., to change leave color, parameter names...).

Slots

graph

The graph in 3 column format originated from the fitted graph.params object

dot.graph

The fitted graph in dot format

score

the score of the model (squared Mahalanobis distance between the observed and fitted basis F-statistics vectors)

bic

The Bayesian Information Criterion associated to the model

fitted.outstats

a matrix containing the target values of the fstats, the fitted values and the Z-score measuring the deviation of the fitted values from the target values in units of standard errors (i.e., Z=(fitted.value-target.value)/se(target.value))

edges.length

a vector containing the estimated edges.length. Note finally, that the (two) edges coming from the roots are assumed of equal length (i.e., unrooted branch) as these are non-identifiable by the method.

edges.length.scaled

If drift.scaling=TRUE, the estimated edges.length in units of t/2N

edges.length.ci

A matrix with two columns (or four columns if drift scaled lengths are computed) containing for each edge length (in a row) the 95% CI lower and higher bounds (columns 3 and 4 containing 95% CI lower and higher bounds of drift scaled lengths, if any)

admix.prop

a vector containing the estimated admixture proportions (if any)

admix.prop.ci

a matrix with two columns containing for each admixture proportion (in a row) the 95% CI lower and higher bounds

nodes.het

The estimated heterozygosities for all nodes (if available; see drift.scaling argument in fit.graph)

fitted.f2.mat

the matrix of all the fitted F2 statistics (obtained from fitted admixture graph parameter values) from which all the fitted fstats can be derived.

optim.results

list containing results of the optim call

See Also

To generate fitted.graph object, see fit.graph.

poolfstat documentation built on April 4, 2025, 1:49 a.m.